From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 Aug 2018 09:06:41 +0000 (+0100)
Subject: JAL-247 draw/print sequence ids now uses common code (unwrapped case)
X-Git-Tag: Release_2_10_5~48
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=b2829c5d7e7815e5e261d39964ade91ed5225510

JAL-247 draw/print sequence ids now uses common code (unwrapped case)
---

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2c5684a..1ac5536 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -48,6 +48,7 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
@@ -942,30 +943,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param pg
-   *          DOCUMENT ME!
-   * @param pwidth
-   *          DOCUMENT ME!
-   * @param pheight
-   *          DOCUMENT ME!
-   * @param pi
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   * 
-   * @throws PrinterException
-   *           DOCUMENT ME!
-   */
-  /**
    * Draws the alignment image, including sequence ids, sequences, and
    * annotation labels and annotations if shown, on either one or two Graphics
-   * context.
+   * contexts.
    * 
    * @param pageWidth
+   *          in pixels
    * @param pageHeight
-   * @param pi
+   *          in pixels
+   * @param pageIndex
+   *          (0, 1, ...)
    * @param idGraphics
    *          the graphics context for sequence ids and annotation labels
    * @param alignmentGraphics
@@ -974,7 +961,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return
    * @throws PrinterException
    */
-  public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+  public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
           Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
@@ -988,8 +975,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             : idWidth;
 
     FontMetrics fm = getFontMetrics(av.getFont());
-    int charHeight = av.getCharHeight();
-    int scaleHeight = charHeight + fm.getDescent();
+    final int charHeight = av.getCharHeight();
+    final int scaleHeight = charHeight + fm.getDescent();
 
     idGraphics.setColor(Color.white);
     idGraphics.fillRect(0, 0, pageWidth, pageHeight);
@@ -998,29 +985,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     /*
      * How many sequences and residues can we fit on a printable page?
      */
-    int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+    final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
 
-    int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+    final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    int alignmentWidth = av.getAlignment().getWidth();
-    int pagesWide = (alignmentWidth / totalRes) + 1;
+    final int alignmentWidth = av.getAlignment().getWidth();
+    final int pagesWide = (alignmentWidth / totalRes) + 1;
 
-    final int startRes = (pi % pagesWide) * totalRes;
-    int endRes = (startRes + totalRes) - 1;
+    final int startRes = (pageIndex % pagesWide) * totalRes;
+    final int endRes = Math.min(startRes + totalRes - 1,
+            alignmentWidth - 1);
 
-    if (endRes > (alignmentWidth - 1))
-    {
-      endRes = alignmentWidth - 1;
-    }
-
-    final int startSeq = (pi / pagesWide) * totalSeq;
-    int endSeq = startSeq + totalSeq;
-
-    int alignmentHeight = av.getAlignment().getHeight();
-    if (endSeq > alignmentHeight)
-    {
-      endSeq = alignmentHeight;
-    }
+    final int startSeq = (pageIndex / pagesWide) * totalSeq;
+    final int alignmentHeight = av.getAlignment().getHeight();
+    final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
 
     int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
 
@@ -1031,7 +1009,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pagesHigh /= pageHeight;
 
-    if (pi >= (pagesWide * pagesHigh))
+    if (pageIndex >= (pagesWide * pagesHigh))
     {
       return Printable.NO_SUCH_PAGE;
     }
@@ -1050,47 +1028,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * then reset to top left (0, 0)
      */
     idGraphics.translate(0, scaleHeight);
-    idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
-    Color currentColor = null;
-    Color currentTextColor = null;
+    IdCanvas idCanvas = getIdPanel().getIdCanvas();
+    List<SequenceI> selection = av.getSelectionGroup() == null ? null
+            : av.getSelectionGroup().getSequences(null);
+    idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+            selection);
 
-    SequenceI seq;
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      seq = av.getAlignment().getSequenceAt(i);
-      if ((av.getSelectionGroup() != null)
-              && av.getSelectionGroup().getSequences(null).contains(seq))
-      {
-        /*
-         * gray out ids of sequences in selection group (if any)
-         */
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getSequenceColour(seq);
-        currentTextColor = Color.black;
-      }
-
-      idGraphics.setColor(currentColor);
-      idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
-              charHeight);
-
-      idGraphics.setColor(currentTextColor);
-
-      int xPos = 0;
-      String displayId = seq.getDisplayId(av.getShowJVSuffix());
-      if (av.isRightAlignIds())
-      {
-        fm = idGraphics.getFontMetrics();
-        xPos = idWidth - fm.stringWidth(displayId) - 4;
-      }
-
-      idGraphics.drawString(displayId, xPos,
-              (((i - startSeq) * charHeight) + charHeight)
-                      - (charHeight / 5));
-    }
     idGraphics.setFont(av.getFont());
     idGraphics.translate(0, -scaleHeight);
 
@@ -1100,7 +1043,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
     getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq);
+            endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index cd7b0b7..484173c 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -63,10 +63,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
   List<SequenceI> searchResults;
 
-  FontMetrics fm;
-
-  AnnotationLabels labels = null;
-
   AnnotationPanel ap;
 
   private Font idfont;
@@ -88,7 +84,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   /**
    * DOCUMENT ME!
    * 
-   * @param gg
+   * @param g
    *          DOCUMENT ME!
    * @param hiddenRows
    *          true - check and display hidden row marker if need be
@@ -101,7 +97,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    * @param ypos
    *          DOCUMENT ME!
    */
-  public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+  public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s,
           int i, int starty, int ypos)
   {
     int xPos = 0;
@@ -110,39 +106,40 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     if ((searchResults != null) && searchResults.contains(s))
     {
-      gg.setColor(Color.black);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+      g.setColor(Color.black);
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.white);
+      g.setColor(Color.white);
     }
     else if ((av.getSelectionGroup() != null)
             && av.getSelectionGroup().getSequences(null).contains(s))
     {
-      gg.setColor(Color.lightGray);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+      g.setColor(Color.lightGray);
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.white);
+      g.setColor(Color.white);
     }
     else
     {
-      gg.setColor(av.getSequenceColour(s));
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+      g.setColor(av.getSequenceColour(s));
+      g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
               charHeight);
-      gg.setColor(Color.black);
+      g.setColor(Color.black);
     }
 
     if (av.isRightAlignIds())
     {
+      FontMetrics fm = g.getFontMetrics();
       xPos = panelWidth
               - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
     }
 
-    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+    g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
             (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
     if (hiddenRows)
     {
-      drawMarker(i, starty, ypos);
+      drawMarker(g, av, i, starty, ypos);
     }
 
   }
@@ -199,7 +196,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     gg.translate(0, transY);
 
-    drawIds(ss, es);
+    drawIds(gg, av, ss, es, searchResults);
 
     gg.translate(0, -transY);
 
@@ -255,37 +252,43 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
     
-    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
+    drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
     
     g.drawImage(image, 0, 0, this);
   }
 
   /**
-   * DOCUMENT ME!
+   * Draws sequence ids from sequence index starty to endy (inclusive), with the
+   * font and other display settings configured on the viewport. Ids of
+   * sequences included in the selection are coloured grey, otherwise the
+   * current id colour for the sequence id is used.
    * 
+   * @param g
+   * @param alignViewport
    * @param starty
-   *          DOCUMENT ME!
    * @param endy
-   *          DOCUMENT ME!
+   * @param selection
    */
-  void drawIds(int starty, int endy)
+  void drawIds(Graphics2D g, AlignViewport alignViewport, final int starty,
+          final int endy, List<SequenceI> selection)
   {
-    if (av.isSeqNameItalics())
+    Font font = alignViewport.getFont();
+    if (alignViewport.isSeqNameItalics())
     {
-      setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
-              av.getFont().getSize()));
+      setIdfont(new Font(font.getName(), Font.ITALIC,
+              font.getSize()));
     }
     else
     {
-      setIdfont(av.getFont());
+      setIdfont(font);
     }
 
-    gg.setFont(getIdfont());
-    fm = gg.getFontMetrics();
+    g.setFont(getIdfont());
+    FontMetrics fm = g.getFontMetrics();
 
-    if (av.antiAlias)
+    if (alignViewport.antiAlias)
     {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+      g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
               RenderingHints.VALUE_ANTIALIAS_ON);
     }
 
@@ -294,37 +297,33 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     boolean hasHiddenRows = av.hasHiddenRows();
 
-    if (av.getWrapAlignment())
+    if (alignViewport.getWrapAlignment())
     {
       drawIdsWrapped(starty, hasHiddenRows);
       return;
     }
 
-    // No need to hang on to labels if we're not wrapped
-    labels = null;
-
     // Now draw the id strings
     int panelWidth = getWidth();
     int xPos = 0;
 
-    SequenceI sequence;
     // Now draw the id strings
     for (int i = starty; i <= endy; i++)
     {
-      sequence = av.getAlignment().getSequenceAt(i);
+      SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
 
       if (sequence == null)
       {
         continue;
       }
 
-      if (hasHiddenRows || av.isDisplayReferenceSeq())
+      if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
       {
-        setHiddenFont(sequence);
+        g.setFont(getHiddenFont(sequence, alignViewport));
       }
 
       // Selected sequence colours
-      if ((searchResults != null) && searchResults.contains(sequence))
+      if (selection != null && selection.contains(sequence))
       {
         currentColor = Color.black;
         currentTextColor = Color.white;
@@ -337,31 +336,32 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       }
       else
       {
-        currentColor = av.getSequenceColour(sequence);
+        currentColor = alignViewport.getSequenceColour(sequence);
         currentTextColor = Color.black;
       }
 
-      gg.setColor(currentColor);
+      g.setColor(currentColor);
 
-      gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
-              av.getCharHeight());
+      int charHeight = alignViewport.getCharHeight();
+      g.fillRect(0, (i - starty) * charHeight,
+              getWidth(), charHeight);
 
-      gg.setColor(currentTextColor);
+      g.setColor(currentTextColor);
 
-      String string = sequence.getDisplayId(av.getShowJVSuffix());
+      String string = sequence
+              .getDisplayId(alignViewport.getShowJVSuffix());
 
-      if (av.isRightAlignIds())
+      if (alignViewport.isRightAlignIds())
       {
         xPos = panelWidth - fm.stringWidth(string) - 4;
       }
 
-      gg.drawString(string, xPos,
-              (((i - starty) * av.getCharHeight()) + av.getCharHeight())
-                      - (av.getCharHeight() / 5));
+      g.drawString(string, xPos, (((i - starty) * charHeight) + charHeight)
+              - (charHeight / 5));
 
       if (hasHiddenRows)
       {
-        drawMarker(i, starty, 0);
+        drawMarker(g, alignViewport, i, starty, 0);
       }
     }
   }
@@ -385,6 +385,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
 
     int annotationHeight = 0;
 
+    AnnotationLabels labels = null;
     if (av.isShowAnnotation())
     {
       if (ap == null)
@@ -393,10 +394,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       }
 
       annotationHeight = ap.adjustPanelHeight();
-      if (labels == null)
-      {
-        labels = new AnnotationLabels(av);
-      }
+      labels = new AnnotationLabels(av);
     }
 
     int hgap = av.getCharHeight();
@@ -424,7 +422,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
         SequenceI s = av.getAlignment().getSequenceAt(i);
         if (hasHiddenRows || av.isDisplayReferenceSeq())
         {
-          setHiddenFont(s);
+          gg.setFont(getHiddenFont(s, av));
         }
         else
         {
@@ -446,18 +444,27 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     }
   }
 
-  void drawMarker(int i, int starty, int yoffset)
+  /**
+   * Draws a marker (a blue right-pointing triangle) between sequences to
+   * indicate hidden sequences.
+   * 
+   * @param g
+   * @param alignViewport
+   * @param seqIndex
+   * @param starty
+   * @param yoffset
+   */
+  void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
   {
-
-    SequenceI[] hseqs = av.getAlignment()
+    SequenceI[] hseqs = alignViewport.getAlignment()
             .getHiddenSequences().hiddenSequences;
     // Use this method here instead of calling hiddenSeq adjust
     // 3 times.
     int hSize = hseqs.length;
 
-    int hiddenIndex = i;
-    int lastIndex = i - 1;
-    int nextIndex = i + 1;
+    int hiddenIndex = seqIndex;
+    int lastIndex = seqIndex - 1;
+    int nextIndex = seqIndex + 1;
 
     for (int j = 0; j < hSize; j++)
     {
@@ -478,52 +485,56 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       }
     }
 
+    /*
+     * are we below or above the hidden sequences?
+     */
     boolean below = (hiddenIndex > lastIndex + 1);
     boolean above = (nextIndex > hiddenIndex + 1);
 
-    gg.setColor(Color.blue);
+    g.setColor(Color.blue);
+    int charHeight = av.getCharHeight();
+
+    /*
+     * vertices of the triangle, below or above hidden seqs
+     */
+    int[] xPoints = new int[]
+    { getWidth() - charHeight,
+        getWidth() - charHeight, getWidth() };
+    int yShift = seqIndex - starty;
+
     if (below)
     {
-      gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(), getWidth() },
-              new int[]
-              { (i - starty) * av.getCharHeight() + yoffset,
-                  (i - starty) * av.getCharHeight() + yoffset
-                          + av.getCharHeight() / 4,
-                  (i - starty) * av.getCharHeight() + yoffset },
-              3);
+      int[] yPoints = new int[] { yShift * charHeight + yoffset,
+          yShift * charHeight + yoffset + charHeight / 4,
+          yShift * charHeight + yoffset };
+      g.fillPolygon(xPoints, yPoints, 3);
     }
     if (above)
     {
-      gg.fillPolygon(
-              new int[]
-              { getWidth() - av.getCharHeight(),
-                  getWidth() - av.getCharHeight(), getWidth() },
-              new int[]
-              { (i - starty + 1) * av.getCharHeight() + yoffset,
-                  (i - starty + 1) * av.getCharHeight() + yoffset
-                          - av.getCharHeight() / 4,
-                  (i - starty + 1) * av.getCharHeight() + yoffset },
-              3);
-
+      yShift++;
+      int[] yPoints = new int[] { yShift * charHeight + yoffset,
+          yShift * charHeight + yoffset - charHeight / 4,
+          yShift * charHeight + yoffset };
+      g.fillPolygon(xPoints, yPoints, 3);
     }
   }
 
-  void setHiddenFont(SequenceI seq)
+  /**
+   * Answers the standard sequence id font, or a bold font if the sequence is
+   * set as reference or a hidden group representative
+   * 
+   * @param seq
+   * @param alignViewport
+   * @return
+   */
+  private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport)
   {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD,
-            av.getFont().getSize());
-
     if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
-      gg.setFont(bold);
-    }
-    else
-    {
-      gg.setFont(getIdfont());
+      return new Font(av.getFont().getName(), Font.BOLD,
+              av.getFont().getSize());
     }
+    return getIdfont();
   }
 
   /**